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fix(python) Fix python model compilation, add to ci, improve hdf5 search, python ci in venv (#337)
* fix(python) Rename dsigmaydp -> dsigma_ydp also in extern declaration * ci(python) Include python-sbml import and simulation in CI (Closes #338) * fix(*) Replace sigma_* by sigma* in all C++ code to have more uniform naming in python- and matlab-generated code * Add missing newly created model files * Fix typo * ci(python) Set exit status according to test outcome (Fixes #339) * ci(python) Disable building python package with cmake-generated libraries until they are repaired to work with current setup.py. Use plain setuptools package. * ci(python) Don't run tests/testSBML.py twice. Is already run as part of scripts/run-codecov.sh -> tests/testCoverage.py * debug(python) Print info if hdf5 was found * feature(python) Check for HDF5 in standard location if pkgconfig is unsuccesful * Fix variable name * added standard osx include and library dir hints * Fix hdf5 library path * Adapt hdf5 library path, be verbose * ci(): List hdf5 files * ci() Maybe we can find the static hdf5 library * ci() List brew hdf5 files * Adapt hdf5 library path * c() Add travis macOS hdf5 directories, remove debug output * fix(cmake) Don't use PYTHON_INCLUDE_PATH which was already deprecated in cmake 3.0.2 or earlier * cmake() VERSION_GREATER_EQUAL only introduced in cmake 3.7, making this check mostly useless * cmake() VERSION_GREATER_EQUAL only introduced in cmake 3.7, making this check mostly useless * Recreate example model code * Revert mingw ::hypot hypot _hypot fix, since ncluding STL headers before Python.h is discouraged This is an open python issue and should be fixed there (python/cpython#880). Windows workarounds exist. * ci(python) Install amici package to virtual environment and run tests there (Closes #342) * cmake() Add target for python source distribution * ci() install h5py * Revert "ci() install h5py" This reverts commit ea79054. * Install h5py in venv * Squashed commit of the following: commit 985646a Author: Daniel Weindl <[email protected]> Date: Tue Jul 3 13:52:18 2018 +0200 ci(python) no --user in venv; install wheel commit f991ce6 Author: Daniel Weindl <[email protected]> Date: Tue Jul 3 13:51:35 2018 +0200 ci(python) no --user in venv; install wheel commit 62f828b Author: Daniel Weindl <[email protected]> Date: Tue Jul 3 13:30:57 2018 +0200 ci(python) install pkgconfig commit b3d37c9 Author: Daniel Weindl <[email protected]> Date: Tue Jul 3 13:21:41 2018 +0200 ci (python) correct package name commit 039ebb0 Author: Daniel Weindl <[email protected]> Date: Tue Jul 3 13:11:55 2018 +0200 ci (python) venv activate commit 49d5412 Author: Daniel Weindl <[email protected]> Date: Tue Jul 3 13:05:03 2018 +0200 ci (python) venv activate commit d1f5824 Author: Daniel Weindl <[email protected]> Date: Tue Jul 3 12:57:45 2018 +0200 ci (python) venv activate commit 1446015 Author: Daniel Weindl <[email protected]> Date: Tue Jul 3 12:49:14 2018 +0200 ci (python) h5py commit b88701d Author: Daniel Weindl <[email protected]> Date: Tue Jul 3 12:42:56 2018 +0200 ci(python) install sdist commit 220323b Author: Daniel Weindl <[email protected]> Date: Tue Jul 3 12:15:40 2018 +0200 ci(python) install --user commit 190a270 Merge: 7adcc83 2e2e445 Author: Fabian Fröhlich <[email protected]> Date: Tue Jul 3 10:02:21 2018 +0200 Merge branch 'master' into feature_venv * ci(python) python 3.6 venv to find proper symengine wheel on osx? * ci(python) install python3.6 * ci(python) install python3.6
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‎.travis.yml

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -38,7 +38,7 @@ matrix:
3838
- brew update # without this homebrew can stumble over wrong ruby version
3939
- travis_wait brew install gcc || brew link --overwrite gcc # fix linker warning regarding /usr/local/include/c++
4040
- brew install hdf5 cppcheck swig doxygen ragel graphviz homebrew/cask/mactex
41-
- brew upgrade python
41+
- brew install zoidbergwill/python/python36
4242
after_success:
4343
- cd $BASE_DIR # cd to base dir for correct relative pah in deploy
4444
deploy:
@@ -65,9 +65,9 @@ install:
6565
- ./scripts/buildAmici.sh
6666

6767
script:
68-
- cd $BASE_DIR/python/sdist
69-
- python3 setup.py sdist --dist-dir=$BASE_DIR/build/python/
70-
- python3 -m pip install $BASE_DIR/build/python/amici-*.tar.gz --verbose
68+
# - cd $BASE_DIR/python/sdist
69+
# - python3 setup.py sdist --dist-dir=$BASE_DIR/build/python/
70+
# - python3 -m pip install $BASE_DIR/build/python/amici-*.tar.gz --verbose
7171
- cd $BASE_DIR
7272
- ./scripts/run-cpputest.sh
7373
- ./scripts/run-cppcheck.sh

‎include/amici/model.h

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -229,14 +229,14 @@ namespace amici {
229229
void fdeltaqB(const int ie, const realtype t, const AmiVector *x, const AmiVector *xB,
230230
const AmiVector *xdot, const AmiVector *xdot_old);
231231

232-
void fsigma_y(const int it, const ExpData *edata, ReturnData *rdata);
232+
void fsigmay(const int it, const ExpData *edata, ReturnData *rdata);
233233

234-
void fdsigma_ydp(const int it, ReturnData *rdata, const ExpData *edata);
234+
void fdsigmaydp(const int it, ReturnData *rdata, const ExpData *edata);
235235

236-
void fsigma_z(const realtype t, const int ie, const int *nroots,
236+
void fsigmaz(const realtype t, const int ie, const int *nroots,
237237
const ExpData *edata, ReturnData *rdata);
238238

239-
void fdsigma_zdp(const realtype t);
239+
void fdsigmazdp(const realtype t);
240240

241241
void fJy(const int it, ReturnData *rdata, const ExpData *edata);
242242

@@ -836,7 +836,7 @@ namespace amici {
836836
* @param p parameter vector
837837
* @param k constant vector
838838
**/
839-
virtual void fsigma_y(realtype *sigmay, const realtype t, const realtype *p, const realtype *k) {
839+
virtual void fsigmay(realtype *sigmay, const realtype t, const realtype *p, const realtype *k) {
840840
throw AmiException("Requested functionality is not supported as (%s) is not implemented for this model!",__func__);
841841
}
842842

@@ -847,7 +847,7 @@ namespace amici {
847847
* @param k constant vector
848848
* @param ip sensitivity index
849849
**/
850-
virtual void fdsigma_ydp(realtype *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) {
850+
virtual void fdsigmaydp(realtype *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) {
851851
throw AmiException("Requested functionality is not supported as (%s) is not implemented for this model!",__func__);
852852
}
853853

@@ -857,7 +857,7 @@ namespace amici {
857857
* @param p parameter vector
858858
* @param k constant vector
859859
**/
860-
virtual void fsigma_z(realtype *sigmaz, const realtype t, const realtype *p, const realtype *k) {
860+
virtual void fsigmaz(realtype *sigmaz, const realtype t, const realtype *p, const realtype *k) {
861861
throw AmiException("Requested functionality is not supported as (%s) is not implemented for this model!",__func__);
862862
}
863863

@@ -868,7 +868,7 @@ namespace amici {
868868
* @param k constant vector
869869
* @param ip sensitivity index
870870
**/
871-
virtual void fdsigma_zdp(realtype *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) {
871+
virtual void fdsigmazdp(realtype *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) {
872872
throw AmiException("Requested functionality is not supported as (%s) is not implemented for this model!",__func__);
873873
}
874874

‎matlab/@amimodel/compileAndLinkModel.m

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -70,7 +70,7 @@ function compileAndLinkModel(modelname, modelSourceFolder, coptim, debug, funs,
7070

7171
%% Model-specific files
7272
for j=1:length(funs)
73-
baseFileName = [modelname '_' funs{j}];
73+
baseFileName = [modelname '_' strrep(funs{j}, 'sigma_', 'sigma')];
7474
cfun(1).(funs{j}) = sourceNeedsRecompilation(modelSourceFolder, modelObjectFolder, baseFileName, objectFileSuffix);
7575
end
7676

@@ -114,6 +114,7 @@ function compileAndLinkModel(modelname, modelSourceFolder, coptim, debug, funs,
114114
end
115115
end
116116
funsForRecompile = funs(structfun(@(x) logical(x), cfun(1)));
117+
funsForRecompile = cellfun(@(x) strrep(x, 'sigma_', 'sigma'), funsForRecompile, 'UniformOutput', false);
117118
end
118119

119120
if(numel(funsForRecompile))
@@ -131,15 +132,15 @@ function compileAndLinkModel(modelname, modelSourceFolder, coptim, debug, funs,
131132

132133
% append model object files
133134
for j=1:length(funs)
134-
filename = fullfile(modelObjectFolder, [modelname '_' funs{j} objectFileSuffix]);
135+
filename = fullfile(modelObjectFolder, [modelname '_' strrep(funs{j}, 'sigma_', 'sigma') objectFileSuffix]);
135136
if(exist(filename,'file'))
136137
objectsstr = strcat(objectsstr,...
137138
' "',filename,'"');
138139
end
139140
end
140141

141142
% compile the wrapfunctions object
142-
fprintf('wrapfunctions | ');
143+
fprintf('wrapfunctions | ');
143144
eval(['mex ' DEBUG COPT ...
144145
' -c -outdir ' modelObjectFolder ' ' ...
145146
fullfile(modelSourceFolder,'wrapfunctions.cpp') ' ' ...

‎matlab/@amimodel/generateC.m

Lines changed: 12 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -17,6 +17,7 @@ function generateC(this)
1717
% write fun ccode
1818

1919
for ifun = this.funs
20+
cppFunctionName = strrep(ifun{1}, 'sigma_', 'sigma');
2021
if(isfield(this.fun,ifun{1}))
2122
bodyNotEmpty = any(this.fun.(ifun{1}).sym(:)~=0);
2223
if(strcmp(ifun{1},'JSparse'))
@@ -28,7 +29,7 @@ function generateC(this)
2829

2930
if(bodyNotEmpty)
3031
fprintf([ifun{1} ' | ']);
31-
fid = fopen(fullfile(this.wrap_path,'models',this.modelname,[this.modelname '_' ifun{1} '.cpp']),'w');
32+
fid = fopen(fullfile(this.wrap_path,'models',this.modelname,[this.modelname '_' cppFunctionName '.cpp']),'w');
3233
fprintf(fid,'\n');
3334
fprintf(fid,'#include "amici/symbolic_functions.h"\n');
3435
fprintf(fid,'#include "amici/defines.h" //realtype definition\n');
@@ -44,7 +45,7 @@ function generateC(this)
4445
fprintf(fid,'\n');
4546

4647
% function definition
47-
fprintf(fid,['void ' ifun{1} '_' this.modelname '' this.fun.(ifun{1}).argstr ' {\n']);
48+
fprintf(fid,['void ' cppFunctionName '_' this.modelname '' this.fun.(ifun{1}).argstr ' {\n']);
4849
if(strcmp(ifun{1},'JSparse'))
4950
for i = 1:length(this.rowvals)
5051
fprintf(fid,[' JSparse->indexvals[' num2str(i-1) '] = ' num2str(this.rowvals(i)) ';\n']);
@@ -132,7 +133,8 @@ function generateC(this)
132133
% access argstr
133134
end
134135
if(checkIfFunctionBodyIsNonEmpty(this,ifun{1}))
135-
fprintf(fid,['extern void ' ifun{1} '_' this.modelname this.fun.(ifun{1}).argstr ';\n']);
136+
cppFunctionName = strrep(ifun{1}, 'sigma_', 'sigma');
137+
fprintf(fid,['extern void ' cppFunctionName '_' this.modelname this.fun.(ifun{1}).argstr ';\n']);
136138
end
137139
end
138140

@@ -180,9 +182,10 @@ function generateC(this)
180182
fprintf(fid,[' const char* getAmiciVersion() const { return "' getCommitHash(fileparts(fileparts(mfilename('fullpath')))) '"; };\n\n']);
181183

182184
for ifun = this.funs
183-
fprintf(fid,[' virtual void f' ifun{1} this.fun.(ifun{1}).argstr ' override {\n']);
185+
cppFunctionName = strrep(ifun{1}, 'sigma_', 'sigma');
186+
fprintf(fid,[' virtual void f' cppFunctionName this.fun.(ifun{1}).argstr ' override {\n']);
184187
if(checkIfFunctionBodyIsNonEmpty(this,ifun{1}))
185-
fprintf(fid,[' ' ifun{1} '_' this.modelname '' removeTypes(this.fun.(ifun{1}).argstr) ';\n']);
188+
fprintf(fid,[' ' cppFunctionName '_' this.modelname '' removeTypes(this.fun.(ifun{1}).argstr) ';\n']);
186189
end
187190
fprintf(fid,' }\n\n');
188191
end
@@ -241,7 +244,8 @@ function generateCMakeFile(this)
241244
for j=1:length(this.funs)
242245
funcName = this.funs{j};
243246
if(checkIfFunctionBodyIsNonEmpty(this,funcName))
244-
sourceStr = [ sourceStr, sprintf('${MODEL_DIR}/%s_%s.cpp\n', this.modelname, funcName) ];
247+
cppFunctionName = strrep(funcName, 'sigma_', 'sigma');
248+
sourceStr = [ sourceStr, sprintf('${MODEL_DIR}/%s_%s.cpp\n', this.modelname, cppFunctionName) ];
245249
end
246250
end
247251

@@ -287,5 +291,6 @@ function generateMainC(this)
287291
function nonempty = checkIfFunctionBodyIsNonEmpty(this,ifun)
288292
% if we don't have symbolic variables, it might have been generated before and symbolic expressions were simply not
289293
% regenerated. any() for empty (no generated) variables is always false.
290-
nonempty = or(exist(fullfile(this.wrap_path,'models',this.modelname,[this.modelname '_' ifun '.cpp']),'file'),any(this.fun.(ifun).sym(:)~=0));
294+
cppFunctionName = strrep(ifun, 'sigma_', 'sigma');
295+
nonempty = or(exist(fullfile(this.wrap_path,'models',this.modelname,[this.modelname '_' cppFunctionName '.cpp']),'file'),any(this.fun.(ifun).sym(:)~=0));
291296
end

‎models/model_dirac/CMakeLists.txt

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -37,7 +37,7 @@ ${MODEL_DIR}/model_dirac_dxdotdp.cpp
3737
${MODEL_DIR}/model_dirac_dydx.cpp
3838
${MODEL_DIR}/model_dirac_qBdot.cpp
3939
${MODEL_DIR}/model_dirac_root.cpp
40-
${MODEL_DIR}/model_dirac_sigma_y.cpp
40+
${MODEL_DIR}/model_dirac_sigmay.cpp
4141
${MODEL_DIR}/model_dirac_stau.cpp
4242
${MODEL_DIR}/model_dirac_sxdot.cpp
4343
${MODEL_DIR}/model_dirac_xBdot.cpp
@@ -69,7 +69,7 @@ endif()
6969
## SWIG
7070
option(ENABLE_SWIG "Build swig/python library?" ON)
7171
if(ENABLE_SWIG)
72-
if(${CMAKE_VERSION} VERSION_GREATER_EQUAL 3.8)
72+
if(NOT(${CMAKE_VERSION} VERSION_LESS 3.8))
7373
add_subdirectory(swig)
7474
else()
7575
message(WARNING "Unable to build SWIG interface, upgrade CMake to >=3.8.")

‎models/model_dirac/model_dirac.h

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#ifndef _amici_model_dirac_h
22
#define _amici_model_dirac_h
3-
/* Generated by amiwrap (R2017b) 32ff5874402bf4335dcd258191c251105e377de4 */
3+
/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
44
#include <cmath>
55
#include <memory>
66
#include "amici/defines.h"
@@ -29,7 +29,7 @@ extern void dxdotdp_model_dirac(realtype *dxdotdp, const realtype t, const realt
2929
extern void dydx_model_dirac(double *dydx, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h);
3030
extern void qBdot_model_dirac(realtype *qBdot, const int ip, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *xB, const realtype *w, const realtype *dwdp);
3131
extern void root_model_dirac(realtype *root, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h);
32-
extern void sigma_y_model_dirac(double *sigmay, const realtype t, const realtype *p, const realtype *k);
32+
extern void sigmay_model_dirac(double *sigmay, const realtype t, const realtype *p, const realtype *k);
3333
extern void stau_model_dirac(double *stau, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *sx, const int ip, const int ie);
3434
extern void sxdot_model_dirac(realtype *sxdot, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const int ip, const realtype *sx, const realtype *w, const realtype *dwdx, const realtype *J, const realtype *dxdotdp);
3535
extern void xBdot_model_dirac(realtype *xBdot, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *xB, const realtype *w, const realtype *dwdx);
@@ -62,7 +62,7 @@ class Model_model_dirac : public amici::Model_ODE {
6262

6363
virtual amici::Model* clone() const override { return new Model_model_dirac(*this); };
6464

65-
const char* getAmiciVersion() const { return "32ff5874402bf4335dcd258191c251105e377de4"; };
65+
const char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
6666

6767
virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
6868
J_model_dirac(J, t, x, p, k, h, w, dwdx);
@@ -142,10 +142,10 @@ class Model_model_dirac : public amici::Model_ODE {
142142
virtual void fdrzdx(double *drzdx, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h) override {
143143
}
144144

145-
virtual void fdsigma_ydp(double *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
145+
virtual void fdsigmaydp(double *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
146146
}
147147

148-
virtual void fdsigma_zdp(double *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
148+
virtual void fdsigmazdp(double *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
149149
}
150150

151151
virtual void fdwdp(realtype *dwdp, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w) override {
@@ -182,11 +182,11 @@ class Model_model_dirac : public amici::Model_ODE {
182182
virtual void frz(double *rz, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h) override {
183183
}
184184

185-
virtual void fsigma_y(double *sigmay, const realtype t, const realtype *p, const realtype *k) override {
186-
sigma_y_model_dirac(sigmay, t, p, k);
185+
virtual void fsigmay(double *sigmay, const realtype t, const realtype *p, const realtype *k) override {
186+
sigmay_model_dirac(sigmay, t, p, k);
187187
}
188188

189-
virtual void fsigma_z(double *sigmaz, const realtype t, const realtype *p, const realtype *k) override {
189+
virtual void fsigmaz(double *sigmaz, const realtype t, const realtype *p, const realtype *k) override {
190190
}
191191

192192
virtual void fsrz(double *srz, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *sx, const int ip) override {

‎models/model_events/model_events_sigma_y.cpp renamed to ‎models/model_dirac/model_dirac_sigmay.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ typedef amici::realtype realtype;
66

77
using namespace amici;
88

9-
void sigma_y_model_events(double *sigmay, const realtype t, const realtype *p, const realtype *k) {
9+
void sigmay_model_dirac(double *sigmay, const realtype t, const realtype *p, const realtype *k) {
1010
sigmay[0] = 1.0;
1111
}
1212

‎models/model_dirac/swig/CMakeLists.txt

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ find_package(SWIG REQUIRED)
44
include(${SWIG_USE_FILE})
55

66
FIND_PACKAGE(PythonLibs REQUIRED)
7-
INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_PATH})
7+
include_directories(${PYTHON_INCLUDE_DIRS})
88

99
SET(CMAKE_SWIG_FLAGS "")
1010
SET_SOURCE_FILES_PROPERTIES(${PROJECT_NAME}.i PROPERTIES CPLUSPLUS ON)

‎models/model_events/CMakeLists.txt

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -46,8 +46,8 @@ ${MODEL_DIR}/model_events_dzdx.cpp
4646
${MODEL_DIR}/model_events_qBdot.cpp
4747
${MODEL_DIR}/model_events_root.cpp
4848
${MODEL_DIR}/model_events_rz.cpp
49-
${MODEL_DIR}/model_events_sigma_y.cpp
50-
${MODEL_DIR}/model_events_sigma_z.cpp
49+
${MODEL_DIR}/model_events_sigmay.cpp
50+
${MODEL_DIR}/model_events_sigmaz.cpp
5151
${MODEL_DIR}/model_events_srz.cpp
5252
${MODEL_DIR}/model_events_stau.cpp
5353
${MODEL_DIR}/model_events_sxdot.cpp
@@ -83,7 +83,7 @@ endif()
8383
## SWIG
8484
option(ENABLE_SWIG "Build swig/python library?" ON)
8585
if(ENABLE_SWIG)
86-
if(${CMAKE_VERSION} VERSION_GREATER_EQUAL 3.8)
86+
if(NOT(${CMAKE_VERSION} VERSION_LESS 3.8))
8787
add_subdirectory(swig)
8888
else()
8989
message(WARNING "Unable to build SWIG interface, upgrade CMake to >=3.8.")

‎models/model_events/model_events.h

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
#ifndef _amici_model_events_h
22
#define _amici_model_events_h
3-
/* Generated by amiwrap (R2017b) 32ff5874402bf4335dcd258191c251105e377de4 */
3+
/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
44
#include <cmath>
55
#include <memory>
66
#include "amici/defines.h"
@@ -38,8 +38,8 @@ extern void dzdx_model_events(double *dzdx, const int ie, const realtype t, cons
3838
extern void qBdot_model_events(realtype *qBdot, const int ip, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *xB, const realtype *w, const realtype *dwdp);
3939
extern void root_model_events(realtype *root, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h);
4040
extern void rz_model_events(double *rz, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h);
41-
extern void sigma_y_model_events(double *sigmay, const realtype t, const realtype *p, const realtype *k);
42-
extern void sigma_z_model_events(double *sigmaz, const realtype t, const realtype *p, const realtype *k);
41+
extern void sigmay_model_events(double *sigmay, const realtype t, const realtype *p, const realtype *k);
42+
extern void sigmaz_model_events(double *sigmaz, const realtype t, const realtype *p, const realtype *k);
4343
extern void srz_model_events(double *srz, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *sx, const int ip);
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extern void stau_model_events(double *stau, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *sx, const int ip, const int ie);
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extern void sxdot_model_events(realtype *sxdot, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const int ip, const realtype *sx, const realtype *w, const realtype *dwdx, const realtype *J, const realtype *dxdotdp);
@@ -76,7 +76,7 @@ class Model_model_events : public amici::Model_ODE {
7676

7777
virtual amici::Model* clone() const override { return new Model_model_events(*this); };
7878

79-
const char* getAmiciVersion() const { return "32ff5874402bf4335dcd258191c251105e377de4"; };
79+
const char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
8080

8181
virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
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J_model_events(J, t, x, p, k, h, w, dwdx);
@@ -162,10 +162,10 @@ class Model_model_events : public amici::Model_ODE {
162162
drzdx_model_events(drzdx, ie, t, x, p, k, h);
163163
}
164164

165-
virtual void fdsigma_ydp(double *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
165+
virtual void fdsigmaydp(double *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
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}
167167

168-
virtual void fdsigma_zdp(double *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
168+
virtual void fdsigmazdp(double *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
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}
170170

171171
virtual void fdwdp(realtype *dwdp, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w) override {
@@ -205,12 +205,12 @@ class Model_model_events : public amici::Model_ODE {
205205
rz_model_events(rz, ie, t, x, p, k, h);
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}
207207

208-
virtual void fsigma_y(double *sigmay, const realtype t, const realtype *p, const realtype *k) override {
209-
sigma_y_model_events(sigmay, t, p, k);
208+
virtual void fsigmay(double *sigmay, const realtype t, const realtype *p, const realtype *k) override {
209+
sigmay_model_events(sigmay, t, p, k);
210210
}
211211

212-
virtual void fsigma_z(double *sigmaz, const realtype t, const realtype *p, const realtype *k) override {
213-
sigma_z_model_events(sigmaz, t, p, k);
212+
virtual void fsigmaz(double *sigmaz, const realtype t, const realtype *p, const realtype *k) override {
213+
sigmaz_model_events(sigmaz, t, p, k);
214214
}
215215

216216
virtual void fsrz(double *srz, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *sx, const int ip) override {

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